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- PDB-6a5d: Crystal structure of plant Glycosylphosphatidylinositol-anchored ... -

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Basic information

Entry
Database: PDB / ID: 6a5d
TitleCrystal structure of plant Glycosylphosphatidylinositol-anchored Protein LLG1
ComponentsGPI-anchored protein LLG1
KeywordsTRANSFERASE / a plant receptor L1
Function / homologyGPI-anchored protein LORELEI-like / pollen tube / positive regulation of growth / plastid / side of membrane / plasma membrane / GPI-anchored protein LLG1
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsXiao, Y. / Chai, J.
CitationJournal: Nature / Year: 2019
Title: Mechanisms of RALF peptide perception by a heterotypic receptor complex.
Authors: Xiao, Y. / Stegmann, M. / Han, Z. / DeFalco, T.A. / Parys, K. / Xu, L. / Belkhadir, Y. / Zipfel, C. / Chai, J.
History
DepositionJun 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GPI-anchored protein LLG1
B: GPI-anchored protein LLG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7554
Polymers29,7282
Non-polymers1,0272
Water4,071226
1
A: GPI-anchored protein LLG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3772
Polymers14,8641
Non-polymers5131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GPI-anchored protein LLG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3772
Polymers14,8641
Non-polymers5131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.212, 66.516, 43.686
Angle α, β, γ (deg.)90.000, 111.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA46 - 138
211chain BB46 - 1003

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Components

#1: Protein GPI-anchored protein LLG1 / LORELEI-like-GPI-anchored protein 1


Mass: 14863.817 Da / Num. of mol.: 2 / Fragment: UNP residues 24-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LLG1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9FKT1
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 513.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 23.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris pH 6.5, 28% Polyethylene glycol 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 35300 / % possible obs: 95.7 % / Redundancy: 4.2 % / Rsym value: 0.096 / Net I/σ(I): 26.6
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 3364 / Rsym value: 0.969

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Processing

Software
NameVersionClassification
REFMAC(1.10.1_2155: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A5E

6a5e


Resolution: 1.401→40.749 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1774 5.03 %
Rwork0.2099 --
obs0.2108 35275 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.81 Å2 / Biso mean: 15.845 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 1.401→40.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 68 226 1732
Biso mean--16.51 24.63 -
Num. residues----186
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A944X-RAY DIFFRACTION2.982TORSIONAL
12B944X-RAY DIFFRACTION2.982TORSIONAL

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